Weak Charge Quantization as an Instanton of Interacting sigma-model

Coulomb blockade in a quantum dot attached to a diffusive conductor is considered in the framework of the non-linear sigma-model. It is shown that the weak charge quantization on the dot is associated with instanton configurations of the Q-field in the conductor. The instantons have a finite action and are replica non--symmetric. It is argued that such instantons may play a role in the transition regime to the interacting insulator.Comment: 4 pages. The 2D case substantially modifie

Statistical Properties of the Reflectance and Transmittance of an Amplifying Random Media

Statistical properties of the transmittance ($T$) and reflectance ($R$) of an amplifying layer with one-dimensional disorder are investigated analytically. Whereas the transmittance at typical realizations decreases exponentially with the layer thickness $L$ just as it does in absorbing media, the average $\left\langle T\right\rangle$ and $\left\langle R\right\rangle$\ are shown to be infinite even for finite $L$ due to the contribution of low-probable resonant realizations corresponding to the non-Gaussian tail of the distribution of $\ln T$. This tail differs drastically from that in the case of absorption. The physical meaning of typical and resonant realizations is discussed.Comment: 5 pages (RevTeX

Two-dimensional array of diffusive SNS junctions with high-transparent interfaces

We report the first comparative study of the properties of two-dimensional arrays and single superconducting film - normal wire - superconducting film (SNS) junctions. The NS interfaces of our SNS junctions are really high transparent, for superconducting and normal metal parts are made from the same material (superconducting polycrystalline PtSi film). We have found that the two-dimensional arrays reveal some novel features: (i) the significant narrowing of the zero bias anomaly (ZBA) in comparison with single SNS junctions, (ii) the appearance of subharmonic energy gap structure (SGS), with up to n=16 (eV=\pm 2\Delta/n), with some numbers being lost, (iii) the transition from 2D logarithmic weak localization behavior to metallic one. Our experiments show that coherent phenomena governed by the Andreev reflection are not only maintained over the macroscopic scale but manifest novel pronounced effects as well. The behavior of the ZBA and SGS in 2D array of SNS junctions strongly suggests that the development of a novel theoretical approach is needed which would self-consistently take into account the distribution of the currents, the potentials, and the superconducting order parameter.Comment: RevTex, 5 pages, 5 figure

Genetics polymorphism of poplars from Moscow region based on high-throughput sequencing of ITS

Poplars are widely used in landscaping of Moscow due to the ability to effectively purify the air from harmful impurities and to release a large amount of oxygen. The genus Populus is characterized by a high level of intraspecies polymorphism, as well as the presence of natural interspecies hybrids. The aim of our work was to evaluate the genetic diversity of poplars, which are growing on the territory of Moscow city by high-throughput sequencing of internal transcribed spacers of 45S rRNA genes (ITS sequences). Sequencing of ITS of 40 poplar plants was performed on Illumina platform (MiSeq) and about 3 000 reads were obtained for each sample in average. Bioinformatics analysis was performed using CLC Genomics Workbench tool. The involved set of poplars had a high level of genetic diversity – the number of single nucleotide polymorphisms (SNPs) detected in each genotype relative to the reference ITS1 and ITS2 sequences of P. trichocarpa varying from 4 to 44. We showed that even trees which had been planted on the same territory and, probably, at the same time had significant genetic differences. It can be speculated that highly polymorphic plant material was used for planting poplars in Moscow. For some sites with SNPs, several variants of nucleotides were found in the same individual and the ratio of SNPs was different. We assume that close to 50/50 ratio is observed in interspecific hybrids due to genetic differences in the ITS sequences between maternal and paternal genotypes. For SNPs with a predominance of one of the variants, the presence of paralogues among numerous genomic copies of ITS sequences is more likely. The results of our work can provide a framework for molecular genetic markers application with the purpose of Populus species and interspecific hybrids identification, determination the origin of a number of natural hybrids, and monitoring the diversity of genus Populus in the Moscow city

Microcirculatory Status and Metabolic Activity of Tissues after Local Administration of Autologous Plasma on the Model of Explosive Soft Tissue Wound in Rats

Background. The possibility of local application of autologous blood plasma (ABP) in soft tissue injuries is currently of particular interest.Objectives. Evaluation of the effects of peri-wound (perifocal) administration of ABP on red blood parameters, microcirculation and oxygen supply of soft tissues of the limb in experimental explosive wound (EW) in rats.Methods. EW was simulated on male Wistar rats (n=146) using a firecracker with a pyrotechnic mixture (patent RU No. 2741238 dated 22.01.2021). Animals were divided into 4 groups: control (2), comparison (1), main (1). The volume of blood loss in explosive wounds was 8 and 15% of the estimated circulating blood volume (CBV) of the animal. Blood was drawn from the rat tail to obtain ABP. 3 hours after the injury, ABP or 0.9% sodium chloride solution was injected intramuscularly into the explosive wound area at a rate of 2.0 ml/kg of animal weight. After 3, 7, 14, 28 days, the number of red blood cells, haemoglobin content, haematocrit were determined in the blood, and microcirculation and oxidative metabolism parameters were determined in the skeletal muscles of the injured area. The data were processed using Microsoft Excel 2013 (Microsoft, USA) and Statistica 10.0 (StatSoft Inc., USA).Results. Blood loss of 8% of the CBV in injured animals did not lead to changes in the quantitative composition of peripheral red blood. After an explosive wound with a blood loss of 15% of the CBV, there was a moderate decrease in the number of red blood cells (from 8.3×1012/l to 6.5×1012/l, p < 0.02), haemoglobin level (from 149.5 g/l to 118 g/l, p < 0.01), haematocrit (from 43.8% to 33.6%, p < 0.01) with recovery by day 7 of observation. The explosive soft tissue wound was characterized by marked post-traumatic microcirculatory disorders irrespective of the amount of blood loss. Perifocal intramuscular administration of ABP in animals with an explosive wound and blood loss of 15% CBV reduced the severity of post-traumatic microcirculatory and oxidative metabolic disorders mainly in the early post-traumatic period, as evidenced by an increase in the perfusion variation coefficient Kv by 1.2–1.3 times (p < 0.05), tissue oxygen consumption U by 20–22% (p < 0.05) and fluorescent oxygen consumption by FPC by 48% (p < 0.05).Conclusion. With an experimental explosive wound of the soft tissues of the thigh in rats, a single early (3 hours after the injury) peri-wound intramuscular administration of ABP reduces the severity of local post-traumatic microcirculatory and metabolic disorders in skeletal muscle

Получение цельноорганного скаффолда печени крысы

Engineering a three-dimensional scaffold opens up great prospects for creation of manufacturing biological artificial organs. The article presents a method of perfusion decellularization of a rat liver, with the main problems and options for their solution being analyzed. Perfusion of a donor liver with 0.1 % a sodium dodecyl sulfate (SDS) solution allows obtaining a high-quality cell-free matrix characterized by preserved hepatic architectonics, patent vascular bed, residual DNA of less than 1 %, no signs of collagen fibers destruction and tissue edema. The obtained scaffold can be used for recellularization by allogeneic cell cultures when creating volumetric tissue-engineered designs.Получение трехмерного скаффолда открывает широкие перспективы для инженерии биоискусственных органов. В работе представлен метод перфузионной децеллюляризации печени крысы с анализом основных проблем и вариантов их решения. Перфузия донорской печени 0,1 %-ным раствором додецилсульфата натрия (SDS) позволяет получить качественный бесклеточный матрикс, характеризующийся сохранностью печеночной архитектоники, проходимостью сосудистого русла, остаточной ДНК менее 1 %, отсутствием признаков деструкции коллагеновых волокон и тканевого отека. Полученный предложенным методом скаффолд может использоваться для рецеллюляризации аллогенными клеточными культурами при создании объемных тканеинженерных конструкций

A Pipeline NanoTRF as a New Tool for De Novo Satellite DNA Identification in the Raw Nanopore Sequencing Reads of Plant Genomes

High-copy tandemly organized repeats (TRs), or satellite DNA, is an important but still enigmatic component of eukaryotic genomes. TRs comprise arrays of multi-copy and highly similar tandem repeats, which makes the elucidation of TRs a very challenging task. Oxford Nanopore sequencing data provide a valuable source of information on TR organization at the single molecule level. However, bioinformatics tools for de novo identification of TRs in raw Nanopore data have not been reported so far. We developed NanoTRF, a new python pipeline for TR repeat identification, characterization and consensus monomer sequence assembly. This new pipeline requires only a raw Nanopore read file from low-depth (<1×) genome sequencing. The program generates an informative html report and figures on TR genome abundance, monomer sequence and monomer length. In addition, NanoTRF performs annotation of transposable elements (TEs) sequences within or near satDNA arrays, and the information can be used to elucidate how TR–TE co-evolve in the genome. Moreover, we validated by FISH that the NanoTRF report is useful for the evaluation of TR chromosome organization—clustered or dispersed. Our findings showed that NanoTRF is a robust method for the de novo identification of satellite repeats in raw Nanopore data without prior read assembly. The obtained sequences can be used in many downstream analyses including genome assembly assistance and gap estimation, chromosome mapping and cytogenetic marker development

Integration of Repeatomic and Cytogenetic Data on Satellite DNA for the Genome Analysis in the Genus <i>Salvia</i> (Lamiaceae)

Within the complicated and controversial taxonomy of cosmopolitan genus Salvia L. (Lamiaceae) are valuable species Salvia officinalis L. and Salvia sclarea L., which are important for the pharmaceutical, ornamental horticulture, food, and perfume industries. Genome organization and chromosome structure of these essential oil species remain insufficiently studied. For the first time, the comparative repeatome analysis of S. officinalis and S. sclarea was performed using the obtained NGS data, RepeatExplorer/TAREAN pipelines and FISH-based chromosome mapping of the revealed satellite DNA families (satDNAs). In repeatomes of these species, LTR retrotransposons made up the majority of their repetitive DNA. Interspecific variations in genome abundance of Class I and Class II transposable elements, ribosomal DNA, and satellite DNA were revealed. Four (S. sclarea) and twelve (S. officinalis) putative satDNAs were identified. Based on patterns of chromosomal distribution of 45S rDNA; 5S rDNA and the revealed satDNAs, karyograms of S. officinalis and S. sclarea were constructed. Promising satDNAs which can be further used as chromosome markers to assess inter- and intraspecific chromosome variability in Salvia karyotypes were determined. The specific localization of homologous satDNA and 45S rDNA on chromosomes of the studied Salvia species confirmed their common origin, which is consistent with previously reported molecular phylogenetic data